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Title: Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Author
item SESHADRI, REKHA - Ag Research Limited
item LEAHY, SINEAD - Ag Research Limited
item ATTWOOD, GRAEME - Ag Research Limited
item HOONG TEH, KOON - Ag Research Limited
item LAMBIE, SUZANNE - Ag Research Limited
item ELOE-FADROSH, EMILY - Department Of Energy Joint Genome
item PAVLOPOULOS, GEORGIOS - Department Of Energy Joint Genome
item HADJITHOMAS, MICHALIS - Department Of Energy Joint Genome
item VARGHESE, NEHA - Department Of Energy Joint Genome
item PALEVICH, NICOLA - Ag Research Limited
item JANSSEN, PETER - Ag Research Limited
item COOKSON, ADRIAN - Ag Research Limited
item NOEL, SAMANTHA - Ag Research Limited
item SONI, PRIYA - Ag Research Limited
item REILLY, KERRI - Ag Research Limited
item ATHERLY, TODD - Ag Research Limited
item ZIEMER, CHERIE - Department Of Energy Joint Genome
item WRIGHT, ANDRE-DENNIS - Aberystwyth University
item ISHAQ, SUZANNE - Aix-Marseille University
item COTTA, MICHAEL - Former ARS Employee
item Thompson, Stephanie
item CROSLEY, KATIE - Institut National De La Recherche Agronomique (INRA)
item MCKAIN, NEST - King Abdulaziz University
item WALLACE, JOHN - King Abdulaziz University
item FLINT, HARRY - King Abdulaziz University
item MARTIN, JENNIFER - King Abdulaziz University
item FORSTER, ROBERT - Lethbridge Research Center
item GRUNINGER, ROBERT J - Lethbridge Research Center
item MCALLISTER, TIM - Lethbridge Research Center
item GILBERT, ROSALIND - Agri-Sciences Queensland
item OUWERKER, DIANE - Agri-Sciences Queensland
item KLIEVE, ATHOL - University Of Queensland
item JASSIM, RAFAT - University Of Queensland
item DENMAN, STUART - Csiro, Black Mountain Laboratories
item MCSWEENEY, CHRIS - Csiro, Black Mountain Laboratories
item ROSEWARNE, CARLY - Csiro, Black Mountain Laboratories
item KOIKE, SATOSHI - Hokkaido University
item KOBAYASHI, YASUO - Hokkaido University
item MITSUMORI, MAKOTO - Hokkaido University
item SHINKAI, TAKUMI - Hokkaido University
item CRAVERO, SILVIO - Instituto Nacional De Tecnologia Agropecuaria
item CERON CUCCHI, MARIA - Instituto Nacional Tecnologia Agropecuaria
item PERRY, RECHELLE - Ag Research Limited
item HENDERSON, GEMMA - Ag Research Limited
item CREEVEY, CHRISTOPHER - Aberystwyth University
item TARRAPON, NICOLAS - Aix-Marseille University
item LAPEBIE, PASCAL - Aix-Marseille University
item DRULA, ELODIE - Aix-Marseille University
item LOMBARD, VINCENT - Aix-Marseille University
item RUBIN, EDWARD - Department Of Energy Joint Genome
item KYRPIDES, NIKOS - Department Of Energy Joint Genome
item HENRISSAT, BERNARD - Aix-Marseille University
item WOYKE, TANJA - Department Of Energy Joint Genome
item IVANOVA, NATALIA - Department Of Energy Joint Genome
item KELLY, WILLIAM - Ag Research Limited

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/1/2017
Publication Date: 3/19/2018
Citation: Seshadri, R., Leahy, S.C., Attwood, G.T., Hoong Teh, K., Lambie, S.C., Eloe-Fadrosh, E.A., Pavlopoulos, G.A, Hadjithomas, M., Varghese, N.J., Paez-Espino, D., Hungate1000 Project Collaborators*: Palevich, N., Janssen,P.H.,Ronimus, R.S., Noel, S., Soni, P., Reilly, K., Atherly, T., Ziemer, C., Wright, A.D., Ishaq, S., Cotta, M., Thompson, S.R., Crosley, K., Mckain, N., Wallace, R.J., Flint, H.J., Martin, J.C., Forster, R.J., Gruninger, R.J., McAllister, T., Gilbert, R., OuwerkerK, D., Klieve, A., Jassim, R.A., Denman, S., McSweeney, C., Rosewarne, C., Koike, S., Kobayashi, Y., Mitsumori, M., Shinkai, T., Cravero, S., Ceron Cucchi, M.*, Perry, R., Henderson, G., Creevey, C.J., Tarrapon, N., Lapebie, P., Drula, E., Lombard, V., Rubin, E., Kyrpides, N.C., Henrissat, B., Woyke, T., Ivanova, N.N, Kelly, W.J. 2018. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology. 36:359-367. doi: 10.1038/nbt.4110.
DOI: https://doi.org/10.1038/nbt.4110

Interpretive Summary: Ruminant animals including domestic cattle, sheep, and goats offer the unique advantage over other livestock of converting low value, lignocellulosic plant material into high value animal proteins in the form of milk, meat and fibre products, via microbial digestion and fermentation in their rumens. Consequently, the rumen represents one of the most rapid and efficient lignocellulose depolymerisation and utilization systems known. Here we present the results from a coordinated effort by rumen microbiology researchers worldwide (the Hungate1000 project) whose aim was to generate a community resource of reference microbial genomes. This genome set has been used to increase understanding of rumen microbes by examining their degradative and physiological potential, determining their occurrence in environmental samples, and identifying potential rumen-specific evolutionary adaptations. These results provide a rich resource to identify alternative antimicrobials and biotechnologically relevant carbohydrate degrading enzymes for use as animal feed additives or application in lignocellulose-based bioconversion processes.

Technical Abstract: Ruminant livestock underpin food security in many regions of the world. Their growth and productivity depend on a symbiotic microbial community within the rumen fermenting plant polysaccharides into nutrients for the host. Here we present a reference set of 410 rumen isolate genomes covering all known major archaeal and bacterial families. We determined the polysaccharide degradative and other metabolic potential of these organisms, assigning unclassified taxa to previously indeterminate functional roles. Examining recruitment of over 8000 metagenome samples from diverse habitats, most species were detected in available rumen samples, however a significant number were also detected in human digestive samples. Comparisons with 388 human intestinal isolate genomes revealed rumen-specific adaptations including the ability to synthesize cofactor vitamin B12 de novo, and ongoing evolution by gene loss of glycolytic enolase. Underrepresentation of markers of oxygen tolerance and sporulation allude that rumen microbes do not encounter environmental stressors to the same extent, supporting the notion of vertical inheritance of the rumen microbiome. This genome collection constitutes a biological resource that can be used to advance our understanding of rumen function, and help find a balance between increased food production and reduced greenhouse gas emissions.